Comparison between the genders for the ages and types¶
Questions
- What are the differences between the gender for the different combinations of ages and types?
- Do we observe the same changes as globally?
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data...
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| M VS F (SPF, 8w) | 2462 | 1291 | 1171 |
| M VS F (GF, 8w) | 2730 | 1419 | 1311 |
| M VS F (SPF, 52w) | 3459 | 1735 | 1724 |
| M VS F (GF, 52w) | 3346 | 1689 | 1657 |
| M VS F (SPF, 104w) | 290 | 148 | 142 |
| M VS F (GF, 104w) | 95 | 40 | 55 |
Differentially expressed genes¶
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”
Comparison of the numbers per ages¶
Differentially expressed genes
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
| Age | SPF | GF |
|---|---|---|
| 8w | M vs F | M vs F |
| 52w | M vs F | M vs F |
| 104w | M vs F | M vs F |
GO analysis¶
Biological process¶
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Network based on description similarity
| Age | SPF | GF |
|---|---|---|
| 8w | M vs F | M vs F |
| 52w | M vs F | M vs F |
| 104w | M vs F | M vs F |
M VS F (SPF, 8w)
M VS F (GF, 8w)
M VS F (SPF, 52w)
M VS F (GF, 52w)
M VS F (SPF, 104w)
M VS F (GF, 104w)
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Warning message: “Removed 6 rows containing missing values (geom_point).”
KEGG pathways¶
[1] "Note: 17 of 5736 unique input IDs unmapped." [1] "Note: 17 of 5736 unique input IDs unmapped."
Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 17 of 5736 unique input IDs unmapped."
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Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/